library(tidyverse)
library(ggplot2)
library(plotly)
library(ggpubr)
df_long <- read_csv("data/GMDD_DATA_long_2021-08-17_1214.csv")
knitr::opts_chunk$set(warning = FALSE, message = FALSE, fig.width = 5, fig.height = 4)
## this function plots a distribution histogram for each variable ********
plot_score <- function(var, vtitle) {
df_long$var <- unlist(df_long[, var])
ggplot(df_long, aes(var)) +
geom_bar() +
theme_minimal() +
xlab("") +
ggtitle(vtitle)
}
## this function creates a line graph for each individual ****************
plot_within <- function (data, fun.y, vtitle) {
data$fun.y <- data[, fun.y]
data$fun.y <- unlist(data$fun.y)
ggplot(data, aes(as.numeric(visit), fun.y, group = record_id, color = record_id)) +
geom_line(alpha = 0.4) +
theme_classic(base_size = 12) +
theme(legend.position = "None") +
labs(title = vtitle) +
ylab("") +
xlab("visit")
}
## this function returns the overall sd for a variable *****************
sd_all <- function(data, var) {
data$var <- data[, var]
data$var <- unlist(data$var)
sd(data$var, na.rm = TRUE)
}
# this function plots the distribution of within-subject sd for a variable,
# and also plots the overall sd ****************************************
plot_within_sd <- function(data, var, vtitle) {
sd_var <- sd_all(data, var)
data$var <- data[, var]
data$var <- unlist(data$var)
sd_within_data <- data %>% group_by(record_id) %>% summarize(sd = sd(var, na.rm = TRUE))
ggplot(sd_within_data, aes(sd)) + geom_density(fill = "lightgrey") +
geom_vline(data = data, xintercept = sd_var) +
theme_minimal() +
ggtitle(vtitle)
}
T18v1.
plot_score("cgi_s", "CGI-S")
plot_within(df_long, "cgi_s", "CGI-S - within")
plot_within_sd(df_long, "cgi_s", "CGI-S - within SD")
T19v1.
plot_score("cirsg_total_score", "CIRS-G: Total")
plot_within(df_long, "cirsg_total_score", "CIRS-G: Total - within")
plot_within_sd(df_long, "cirsg_total_score", "CIRS-G: Total - within SD")
T19v2.
plot_score("cirsg_severity_index", "CIRS-G: Severity Index")
plot_within(df_long, "cirsg_severity_index", "CIRS-G: Severity Index - within")
plot_within_sd(df_long, "cirsg_severity_index", "CIRS-G: Severity Index - within SD")
T19v3.
plot_score("cirsg_level3_severity", "CIRS-G: Level 3 severity")
plot_within(df_long, "cirsg_level3_severity", "CIRS-G: Level 3 severity - within")
plot_within_sd(df_long, "cirsg_level3_severity", "CIRS-G: Level 3 severity - within SD")
T19v4.
plot_score("cirsg_level4_severity", "CIRS-G: Level 4 severity")
plot_within(df_long, "cirsg_level4_severity", "CIRS-G: Level 4 severity - within")
plot_within_sd(df_long, "cirsg_level4_severity", "CIRS-G: Level 4 severity - within SD")
T20v1.
plot_score("srfpc_total", "SRFPC: Total")
plot_within(df_long, "srfpc_total", "SRFPC: Total - within")
plot_within_sd(df_long, "srfpc_total", "SRFPC: Total - within SD")
T22v1.
plot_score("cerad_bnt_total", "BNT Total")
plot_within(df_long, "cerad_bnt_total", "BNT Total - within")
plot_within_sd(df_long, "cerad_bnt_total", "BNT Total - within SD")
T22v2.
plot_score("cerad_cp_total", "Constructional Praxis Total")
plot_within(df_long, "cerad_cp_total", "Constructional Praxis Total - within")
plot_within_sd(df_long, "cerad_cp_total", "Constructional Praxis Total - within SD")
T22v3.
plot_score("cerad_wlrec_total", "Word List Recognition Total")
plot_within(df_long, "cerad_wlrec_total", "Word List Recognition Total - within")
plot_within_sd(df_long, "cerad_wlrec_total", "Word List Recognition Total - within SD")
T22v4.
plot_score("cerad_cpr_total", "Constructional Praxis Recall Total")
plot_within(df_long, "cerad_cpr_total", "Constructional Praxis Recall Total - within")
plot_within_sd(df_long, "cerad_cpr_total", "Constructional Praxis Recall Total - within SD")
T23v1.
plot_score("gng_conflict", "GNG: Conflict")
plot_within(df_long, "gng_conflict", "GNG: Conflict - within")
plot_within_sd(df_long, "gng_conflict", "GNG: Conflict - within SD")
T23v2.
plot_score("gng_inhibit", "GNG: Inhibit")
plot_within(df_long, "gng_inhibit", "GNG: Inhibit - within")
plot_within_sd(df_long, "gng_inhibit", "GNG: Inhibit - within SD")
T24v1.
plot_score("panas_positive", "PANAS: Positive")
plot_within(df_long, "panas_positive", "PANAS: Positive - within")
plot_within_sd(df_long, "panas_positive", "PANAS: Positive - within SD")
T24v2.
plot_score("panas_negative", "PANAS: Negative")
plot_within(df_long, "panas_negative", "PANAS: Negative - within")
plot_within_sd(df_long, "panas_negative", "PANAS: Negative - within SD")
T25v1.
plot_score("gds_total", "GDS: Total")
plot_within(df_long, "gds_total", "GDS: Total - within")
plot_within_sd(df_long, "gds_total", "GDS: Total - within SD")
T26v1.
plot_score("gad_total", "GAD: Total")
plot_within(df_long, "gad_total", "GAD: Total - within")
plot_within_sd(df_long, "gad_total", "GAD: Total - within SD")
T26v2.
plot_score("gad_difficulty", "GAD: Difficulty")
plot_within(df_long, "gad_difficulty", "GAD: Difficulty - within")
plot_within_sd(df_long, "gad_difficulty", "GAD: Difficulty - within SD")
T27v1.
plot_score("whodas_s_sum", "WHODAS: Sum")
plot_within(df_long, "whodas_s_sum", "WHODAS: Sum - within")
plot_within_sd(df_long, "whodas_s_sum", "WHODAS: Sum - within SD")
T28v1.
plot_score("faster_total", "FAST-ER: Total")
plot_within(df_long, "faster_total", "FAST-ER: Total - within")
plot_within_sd(df_long, "faster_total", "FAST-ER: Total - within SD")
T29v1.
plot_score("fasd_total", "FAS-D: Total")
plot_within(df_long, "fasd_total", "FAS-D: Total - within")
plot_within_sd(df_long, "fasd_total", "FAS-D: Total - within SD")
T29v2.
plot_score("fasd_total_experience", "FAS-D: Total Experience")
plot_within(df_long, "fasd_total_experience", "FAS-D: Total Experience - within")
plot_within_sd(df_long, "fasd_total_experience", "FAS-D: Total Experience - within SD")
T29v3.
plot_score("fasd_total_impact", "FAS-D: Total Impact")
plot_within(df_long, "fasd_total_impact", "FAS-D: Total Impact - within")
plot_within_sd(df_long, "fasd_total_impact", "FAS-D: Total Impact - within SD")
T30v1.
plot_score("spirituality_i_total", "Spirituality I: Total")
plot_within(df_long, "spirituality_i_total", "Spirituality I: Total - within")
plot_within_sd(df_long, "spirituality_i_total", "Spirituality I: Total - within SD")
T30v2.
plot_score("spirituality_ii_trust", "Spirituality II: Trust")
plot_within(df_long, "spirituality_ii_trust", "Spirituality II: Trust - within")
plot_within_sd(df_long, "spirituality_ii_trust", "Spirituality II: Trust - within SD")
T30v3.
plot_score("spirituality_ii_mistrust", "Spirituality II: Mistrust")
plot_within(df_long, "spirituality_ii_mistrust", "Spirituality II: Mistrust - within")
plot_within_sd(df_long, "spirituality_ii_mistrust", "Spirituality II: Mistrust - within SD")
T30v4.
plot_score("spirituality_iii_total", "Spirituality III: Total")
plot_within(df_long, "spirituality_iii_total", "Spirituality III: Total - within")
plot_within_sd(df_long, "spirituality_iii_total", "Spirituality III: Total - within SD")
T30v5.
plot_score("spitituality_iv_positive", "Spirituality IV: Positive")
plot_within(df_long, "spitituality_iv_positive", "Spirituality IV: Positive - within")
plot_within_sd(df_long, "spitituality_iv_positive", "Spirituality IV: Positive - within SD")
T30v6.
plot_score("spitituality_iv_negative", "Spirituality IV: Negative")
plot_within(df_long, "spitituality_iv_negative", "Spirituality IV: Negative - within")
plot_within_sd(df_long, "spitituality_iv_negative", "Spirituality IV: Negative - within SD")
T31v1.
plot_score("gas_total", "GAS: Total")
plot_within(df_long, "gas_total", "GAS: Total - within")
plot_within_sd(df_long, "gas_total", "GAS: Total - within SD")
T31v2.
plot_score("gas_somatic", "GAS: Somatic")
plot_within(df_long, "gas_somatic", "GAS: Somatic - within")
plot_within_sd(df_long, "gas_somatic", "GAS: Somatic - within SD")
T31v3.
plot_score("gas_cognitive", "GAS: Cognitive")
plot_within(df_long, "gas_cognitive", "GAS: Cognitive - within")
plot_within_sd(df_long, "gas_cognitive", "GAS: Cognitive - within SD")
T31v4.
plot_score("gas_affective", "GAS: Affective")
plot_within(df_long, "gas_affective", "GAS: Affective - within")
plot_within_sd(df_long, "gas_affective", "GAS: Affective - within SD")
T32v1.
plot_score("psqi_global_score", "PSQI: Total")
plot_within(df_long, "psqi_global_score", "PSQI: Total - within")
plot_within_sd(df_long, "psqi_global_score", "PSQI: Total - within SD")
T33v1.
plot_score("pai_scz_total_t", "PAI SCZ: Total (t value)")
plot_within(df_long, "pai_scz_total_t", "PAI SCZ: Total (t value) - within")
plot_within_sd(df_long, "pai_scz_total_t", "PAI SCZ: Total (t value) - within SD")
T33v2.
plot_score("pai_scz_psychexp_t", "PAI SCZ: Psychotic Experiences (t value)")
plot_within(df_long, "pai_scz_psychexp_t", "PAI SCZ: Psychotic Experiences (t value) - within")
plot_within_sd(df_long, "pai_scz_psychexp_t", "PAI SCZ: Psychotic Experiences (t value) - within SD")
T33v3.
plot_score("pai_scz_thought_t", "PAI SCZ: Thought Disorder (t value)")
plot_within(df_long, "pai_scz_thought_t", "PAI SCZ: Thought Disorder (t value) - within")
plot_within_sd(df_long, "pai_scz_thought_t", "PAI SCZ: Thought Disorder (t value) - within SD")
T33v4.
T34v1.
plot_score("mmq_total", "MMQ: Total")
plot_within(df_long, "mmq_total", "MMQ: Total - within")
plot_within_sd(df_long, "mmq_total", "MMQ: Total - within SD")
Social Perception: Affect Naming Total
T21v2.